I was curious about your commonly used weighted LCA parameters, specifically the % to cover (default is 80%) and top % (default is 10%).
Do you usually use the default or after which criteria do you adjust these?
How much biological sense do the default values make - how were this derived?
I am seeing quite some differences of changing these parameters especially in the depth of taxonomic classification of a read. But which depth makes most sense, or how would I know if my read can really be classified to the species level. I am also working with functional genes who really have different taxonomic similarity cutoffs on each taxonomic level…